Job ID = 12531523 SRX = SRX2997376 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5585385 spots for SRR5819451/SRR5819451.sra Written 5585385 spots for SRR5819451/SRR5819451.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:06 5585385 reads; of these: 5585385 (100.00%) were paired; of these: 2729809 (48.87%) aligned concordantly 0 times 1869550 (33.47%) aligned concordantly exactly 1 time 986026 (17.65%) aligned concordantly >1 times ---- 2729809 pairs aligned concordantly 0 times; of these: 406367 (14.89%) aligned discordantly 1 time ---- 2323442 pairs aligned 0 times concordantly or discordantly; of these: 4646884 mates make up the pairs; of these: 4009391 (86.28%) aligned 0 times 111884 (2.41%) aligned exactly 1 time 525609 (11.31%) aligned >1 times 64.11% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 776653 / 3226402 = 0.2407 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:09:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 17 Apr 2021 08:09:09: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:09:09: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:09:15: 1000000 INFO @ Sat, 17 Apr 2021 08:09:22: 2000000 INFO @ Sat, 17 Apr 2021 08:09:29: 3000000 INFO @ Sat, 17 Apr 2021 08:09:35: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 17 Apr 2021 08:09:39: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:09:39: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:09:42: 5000000 INFO @ Sat, 17 Apr 2021 08:09:46: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:09:46: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:09:46: #1 total tags in treatment: 2156949 INFO @ Sat, 17 Apr 2021 08:09:46: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:09:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:09:46: #1 tags after filtering in treatment: 1166595 INFO @ Sat, 17 Apr 2021 08:09:46: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 17 Apr 2021 08:09:46: #1 finished! INFO @ Sat, 17 Apr 2021 08:09:46: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:09:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:09:46: #2 number of paired peaks: 307 WARNING @ Sat, 17 Apr 2021 08:09:46: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sat, 17 Apr 2021 08:09:46: start model_add_line... INFO @ Sat, 17 Apr 2021 08:09:46: start X-correlation... INFO @ Sat, 17 Apr 2021 08:09:46: end of X-cor INFO @ Sat, 17 Apr 2021 08:09:46: #2 finished! INFO @ Sat, 17 Apr 2021 08:09:46: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 08:09:46: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 08:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.05_model.r WARNING @ Sat, 17 Apr 2021 08:09:46: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:09:46: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 08:09:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:09:46: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:09:46: 1000000 INFO @ Sat, 17 Apr 2021 08:09:49: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:09:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:09:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:09:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.05_summits.bed INFO @ Sat, 17 Apr 2021 08:09:51: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (2174 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:09:53: 2000000 INFO @ Sat, 17 Apr 2021 08:10:00: 3000000 INFO @ Sat, 17 Apr 2021 08:10:06: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 17 Apr 2021 08:10:09: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:10:09: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:10:13: 5000000 INFO @ Sat, 17 Apr 2021 08:10:17: 1000000 INFO @ Sat, 17 Apr 2021 08:10:18: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:10:18: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:10:18: #1 total tags in treatment: 2156949 INFO @ Sat, 17 Apr 2021 08:10:18: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:10:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:10:18: #1 tags after filtering in treatment: 1166595 INFO @ Sat, 17 Apr 2021 08:10:18: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 17 Apr 2021 08:10:18: #1 finished! INFO @ Sat, 17 Apr 2021 08:10:18: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:10:18: #2 number of paired peaks: 307 WARNING @ Sat, 17 Apr 2021 08:10:18: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sat, 17 Apr 2021 08:10:18: start model_add_line... INFO @ Sat, 17 Apr 2021 08:10:18: start X-correlation... INFO @ Sat, 17 Apr 2021 08:10:18: end of X-cor INFO @ Sat, 17 Apr 2021 08:10:18: #2 finished! INFO @ Sat, 17 Apr 2021 08:10:18: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 08:10:18: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 08:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.10_model.r WARNING @ Sat, 17 Apr 2021 08:10:18: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:10:18: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 08:10:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:10:18: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:10:21: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:10:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:10:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:10:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.10_summits.bed INFO @ Sat, 17 Apr 2021 08:10:22: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1281 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:10:24: 2000000 INFO @ Sat, 17 Apr 2021 08:10:30: 3000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:10:37: 4000000 INFO @ Sat, 17 Apr 2021 08:10:44: 5000000 INFO @ Sat, 17 Apr 2021 08:10:48: #1 tag size is determined as 76 bps INFO @ Sat, 17 Apr 2021 08:10:48: #1 tag size = 76 INFO @ Sat, 17 Apr 2021 08:10:48: #1 total tags in treatment: 2156949 INFO @ Sat, 17 Apr 2021 08:10:48: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:10:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:10:48: #1 tags after filtering in treatment: 1166595 INFO @ Sat, 17 Apr 2021 08:10:48: #1 Redundant rate of treatment: 0.46 INFO @ Sat, 17 Apr 2021 08:10:48: #1 finished! INFO @ Sat, 17 Apr 2021 08:10:48: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:10:48: #2 number of paired peaks: 307 WARNING @ Sat, 17 Apr 2021 08:10:48: Fewer paired peaks (307) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 307 pairs to build model! INFO @ Sat, 17 Apr 2021 08:10:48: start model_add_line... INFO @ Sat, 17 Apr 2021 08:10:48: start X-correlation... INFO @ Sat, 17 Apr 2021 08:10:48: end of X-cor INFO @ Sat, 17 Apr 2021 08:10:48: #2 finished! INFO @ Sat, 17 Apr 2021 08:10:48: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 08:10:48: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 08:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.20_model.r WARNING @ Sat, 17 Apr 2021 08:10:48: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:10:48: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 08:10:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:10:48: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:10:51: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2997376/SRX2997376.20_summits.bed INFO @ Sat, 17 Apr 2021 08:10:52: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 3 millis CompletedMACS2peakCalling